This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Molecular nanomachinery utilized in biological systems involves interplay between different molecular components performing specific functions. The interactions between these components and their internal conformational preferences are both dynamic, and can also be sensitive to atomic level changes in individual nucleotides or amino acids. For each macromolecule, the gap between visualizing its structure and understanding its functional properties needs to be traversed by a description of the conformational free energy landscape governing its activity. Molecular dynamics (MD) simulations describing these nanomachines at atomic level of detail are perfectly suited to analyzing the dynamical nature of the molecular recognition processes involved. In the present grant, free energy landscape determination through MD simulation methods will be used to understand the recognition of the 3'dinucleotide overhang of siRNA by the PAZ domain in the RNAi meachinery and elucidate the mechanism of error-prone strand propagation by Y-family DNA polymerases.